apaydin's library 633 articles Export

	Simultaneous prediction of protein folding and docking at high resolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 18978-18983. by Rhiju Das, Ingemar AndrÃ©, Yang Shen, et al.Yibing Wu, Alexander Lemak, Sonal Bansal, Cheryl H. Arrowsmith, Thomas Szyperski, David Baker posted to protein_folding docking by apaydin on 2009-11-11 16:27:06 as along with 4 people ahmetbakan paulschlesinger ibuch zwang
	How to mark off paths on the protein energy landscape [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 18879-18880. by Martin Gruebele posted to protein folding energy_landscape by apaydin on 2009-11-11 16:26:43 as
	Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 19011-19016. by Frank NoÃ©, Christof SchÃ¼tte, Eric Vanden-Eijnden, Lothar Reich, Thomas R. Weikl posted to protein folding by apaydin on 2009-11-11 16:18:08 as along with 1 person Diego_Prada
	Physical arguments for distance-weighted interactions in elastic network models for proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. E128-E128. by Konrad Hinsen posted to network model elastic by apaydin on 2009-11-11 16:14:14 as along with 1 person Diego_Prada
	Generating Multiple Solutions for Mixed Integer Programming Problems [My Copy] Integer Programming and Combinatorial Optimization (2007), pp. 280-294. by Emilie Danna, Mary Fenelon, Zonghao Gu, Roland Wunderling posted to programming nmr linear integer diversity assignments by apaydin on 2009-11-08 10:43:29 as
	Experiments concerning sequential versus simultaneous maximization of objective function and distance [My Copy] Journal of Heuristics, Vol. 14, No. 6. (1 December 2008), pp. 613-625. by Peter Greistorfer, Arne Løkketangen, Stefan Voß, David Woodruff posted to programming linear integer diversity by apaydin on 2009-11-08 10:36:47 as along with 1 person and 1 group nojhan Optimization
	Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Nurit Haspel, Brian V. Geisbrecht, John Lambris, Lydia Kavraki posted to multiscale energy_landscape by apaydin on 2009-11-08 08:16:51 as
	PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2743-2744. by T. Aleksiev, R. Potestio, F. Pontiggia, S. Cozzini, C. Micheletti posted to rigidity protein_structure by apaydin on 2009-11-08 07:58:36 as along with 1 person and 1 group oteri Structural Biology Group TorVergata
	Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (30 October 2009), 365. by Stefano Lise, Cedric Archambeau, Massimiliano Pontil, David Jones posted to protein_protein_binding prediction hotspot by apaydin on 2009-11-08 07:57:00 as along with 6 people and 1 group sillitoe kshameer zwang phoenixzxl higueruelo neils Orengo Group Journal Picks
	Structure-Based Predictive Models for Allosteric Hot Spots [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000531. by Omar N. A. Demerdash, Michael D. Daily, Julie C. Mitchell posted to allostery by apaydin on 2009-11-08 07:55:47 as along with 3 people and 1 group nickolay klexa barry McCammon
	Structural relationships among proteins with different global topologies and their implications for function annotation strategies [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 41. (13 October 2009), pp. 17377-17382. by Donald Petrey, Markus Fischer, Barry Honig posted to structural alignment by apaydin on 2009-11-08 07:45:55 as along with 5 people and 1 group philcarter carlosjavierna TRHvidsten zwang phoenixzxl Orengo Group Journal Picks
	Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach. [My Copy] Journal of molecular biology, Vol. 243, No. 4. (4 November 1994), pp. 696-718. by P. J. Kraulis posted to protein_structure_determination 4d-noesy by apaydin on 2009-10-21 16:51:59 as along with 1 person pekrau
	Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides. [My Copy] Proteins (7 July 2009) by Hernán Stamati, Cecilia Clementi, Lydia E. Kavraki posted to peptides landscape dimensionality_reduction conformational by apaydin on 2009-10-20 20:02:21 as
	Protein structure calculation with data imputation: the use of substitute restraints [My Copy] Journal of Biomolecular NMR, Vol. 45, No. 4. (1 December 2009), pp. 397-411. by Carolina Cano, Konrad Brunner, Kumaran Baskaran, Ralph Elsner, Claudia Munte, Hans Kalbitzer posted to protein_structure_determination noe nmr by apaydin on 2009-10-19 20:06:42 as along with 1 person kumar_physics
	Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE) [My Copy] Journal of Biomolecular NMR, Vol. 23, No. 4. (1 August 2002), pp. 271-287. by Wolfram Gronwald, Sherif Moussa, Ralph Elsner, et al.Astrid Jung, Bernhard Ganslmeier, Jochen Trenner, Werner Kremer, Klaus-Peter Neidig, Hans R. Kalbitzer posted to noe_assignment nmr by apaydin on 2009-10-19 14:30:46 as along with 1 person kumar_physics
	Automated combined assignment of NOESY spectra and three-dimensional protein structure determination [My Copy] Journal of Biomolecular NMR, Vol. 10, No. 4. (21 December 1997), pp. 351-362. by Christian Mumenthaler, Peter Güntert, Werner Braun, Kurt Wüthrich posted to protein_structure_determination noe_assignment nmr by apaydin on 2009-10-18 20:24:12 as
	Protein NMR Structure Determination with Automated NOE Assignment Using the New Software CANDID and the Torsion Angle Dynamics Algorithm DYANA [My Copy] Journal of Molecular Biology, Vol. 319, No. 1. (24 May 2002), pp. 209-227. by Torsten Herrmann, Peter Güntert, Kurt Wüthrich posted to protein_structure_determination noe_assignment nmr by apaydin on 2009-10-15 20:00:15 as along with 3 people kumar_physics stharward lna
	The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries [My Copy] Journal of Biomolecular NMR, Vol. 45, No. 4. (1 December 2009), pp. 389-396. by Jurgen Doreleijers, Wim Vranken, Christopher Schulte, et al.Jundong Lin, Jonathan Wedell, Christopher Penkett, Geerten Vuister, Gert Vriend, John Markley, Eldon Ulrich posted to nmr database by apaydin on 2009-10-14 20:06:10 as along with 1 person viktor21614
	Stochastic dynamics of model proteins on a directed graph. [My Copy] Physical review. E, Statistical, nonlinear, and soft matter physics, Vol. 79, No. 6 Pt 1. (June 2009) by Lorenzo Bongini, Lapo Casetti, Roberto Livi, Antonio Politi, Alessandro Torcini posted to protein_folding graph_representation by apaydin on 2009-10-04 18:04:40 as
	The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14349-14354. by Ahmet Bakan, Ivet Bahar posted to protein_dynamics ligand_binding by apaydin on 2009-10-04 18:02:10 as along with 5 people and 1 group ahmetbakan anuragsethi jmccammon okapi boris_aguilar McCammon
	Perspectives on NMR in drug discovery: a technique comes of age [My Copy] Nature Reviews Drug Discovery, Vol. 7, No. 9. (01 September 2008), pp. 738-745. by Maurizio Pellecchia, Ivano Bertini, David Cowburn, et al.Claudio Dalvit, Ernest Giralt, Wolfgang Jahnke, Thomas L. James, Steve W. Homans, Horst Kessler, Claudio Luchinat, Bernd Meyer, Hartmut Oschkinat, Jeff Peng, Harald Schwalbe, Gregg Siegal posted to review nmr drug_discovery by apaydin on 2009-10-03 19:11:09 as along with 1 person ubcg08l
	CASD-NMR: critical assessment of automated structure determination by NMR [My Copy] Nat Meth, Vol. 6, No. 9. (01 September 2009), pp. 625-626. by Antonio Rosato, Anurag Bagaria, David Baker, et al.Benjamin Bardiaux, Andrea Cavalli, Jurgen F. Doreleijers, Andrea Giachetti, Paul Guerry, Peter Guntert, Torsten Herrmann, Yuanpeng J. Huang, Hendrik R. A. Jonker, Binchen Mao, Therese E. Malliavin, Gaetano T. Montelione, Michael Nilges, Srivatsan Raman, Gijs van der Schot, Wim F. Vranken, Geerten W. Vuister, Alexandre M. J. J. Bonvin posted to nmr contacts by apaydin on 2009-09-13 13:58:00 as
	A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations. [My Copy] Proteins, Vol. 77, No. 4. (December 2009), pp. 927-939. by Lin Liu, Leonardus M. Koharudin, Angela M. Gronenborn, Ivet Bahar posted to x-ray nmr gnm ensembles by apaydin on 2009-09-04 18:41:23 as along with 2 people sobolevnrm ahmetbakan
	A Hybrid Approach to Intricate Motion, Manipulation and Task Planning [My Copy] The International Journal of Robotics Research, Vol. 28, No. 1. (1 January 2009), pp. 104-126. by Stephane Cambon, Rachid Alami, Fabien Gravot posted to task_planning planning motion manipulation_planning by apaydin on 2009-08-25 07:06:50 as
	PR-CALC: a program for the reconstruction of NMR spectra from projections. [My Copy] Journal of biomolecular NMR, Vol. 34, No. 3. (March 2006), pp. 179-195. by Brian E. Coggins, Pei Zhou posted to nmr 4d-noesy by apaydin on 2009-08-22 14:34:03 as
	Filtered backprojection for the reconstruction of a high-resolution (4,2)D CH3-NH NOESY spectrum on a 29 kDa protein. [My Copy] Journal of the American Chemical Society, Vol. 127, No. 33. (24 August 2005), pp. 11562-11563. by Brian E. Coggins, Ronald A. Venters, Pei Zhou posted to nmr 4d-noesy by apaydin on 2009-08-22 14:32:24 as
	Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 26. (30 June 2009), pp. 10505-10510. by Prasad V. Burra, Ying Zhang, Adam Godzik, Boguslaw Stec posted to protein_structure by apaydin on 2009-08-17 15:26:23 as along with 6 people and 1 group ubcg08l sobolevnrm philcarter aalibes TRHvidsten zwang Orengo Group Journal Picks
	Computing protein stabilities from their chain lengths. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 26. (30 June 2009), pp. 10649-10654. by Kingshuk Ghosh, Ken A. Dill posted to protein_stability by apaydin on 2009-08-17 15:17:39 as along with 4 people kintoki carlosjavierna sobolevnrm kevinchannon
	Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 29. (21 July 2009), pp. 11837-11844. by Hoi S. Chung, John M. Louis, William A. Eaton posted to protein_folding by apaydin on 2009-08-17 15:13:16 as along with 5 people and 1 group yanjiang doktornoe quanwang paulschlesinger samjlord moernerlab
	Protein elastic network models and the ranges of cooperativity [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 30. (28 July 2009), pp. 12347-12352. by Lei Yang, Guang Song, Robert L. Jernigan posted to normal_mode_analysis by apaydin on 2009-08-17 15:11:59 as along with 4 people Diego_Prada anuragsethi sobolevnrm edws
	PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2085-2087. by Woonghee Lee, William M. Westler, Arash Bahrami, Hamid R. Eghbalnia, John L. Markley posted to visualization nmr assignments by apaydin on 2009-08-17 11:51:49 as
	A topical issue: NMR investigations of molecular dynamics [My Copy] Journal of Biomolecular NMR by Arthur Palmer posted to nmr molecular_dynamics by apaydin on 2009-08-17 11:43:58 as
	Recent advances in computer-aided drug design [My Copy] Brief Bioinform, Vol. 10, No. 5. (1 September 2009), pp. 579-591. by Chun M. Song, Shen J. Lim, Joo C. Tong posted to review drug_design by apaydin on 2009-08-17 11:39:28 as along with 7 people and 1 group mtruksa npt11tpn abhishek_tiwari reyez operon kshameer phoenixzxl structural_bioinformatics
	Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta [My Copy] Journal of Molecular Biology (08 July 2009) by Frank Dimaio, Michael D. Tyka, Matthew L. Baker, Wah Chiu, David Baker posted to electron_microscopy protein_structure_prediction by apaydin on 2009-08-07 06:13:45 as along with 2 people and 2 groups barry reyez structural_bioinformatics McCammon
	On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Zhenxing Liu, Jie Chen, D. Thirumalai posted to allostery by apaydin on 2009-08-07 05:50:35 as
	New Monte Carlo algorithms for protein folding. [My Copy] Current opinion in structural biology, Vol. 9, No. 2. (April 1999), pp. 177-183. by U. H. Hansmann, Y. Okamoto posted to monte_carlo protein_folding by apaydin on 2009-08-05 07:26:50 as along with 6 people flbarroso dgront rabio insectopalo iantunbridge nigham
	Molecular mechanics methods for predicting protein-ligand binding. [My Copy] Physical chemistry chemical physics : PCCP, Vol. 8, No. 44. (28 November 2006), pp. 5166-5177. by Niu Huang, Chakrapani Kalyanaraman, Katarzyna Bernacki, Matthew P. Jacobson posted to ligand-protein-binding molecular_mechanics by apaydin on 2009-08-05 07:26:14 as along with 4 people anuragsethi mijogiffin ucbcjbm superpyrin
	Application of the multiensemble sampling to the equilibrium folding of proteins. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 15. (1 August 2006), pp. 1832-1837. by Hyeon S. Son, Seung-Yeon Y. Kim, Jooyoung Lee, Kyu-Kwang K. Han posted to equilibrium protein_folding by apaydin on 2009-08-05 07:25:22 as
	A Quick Guide to Organizing Computational Biology Projects [My Copy] PLoS Comput Biol, Vol. 5, No. 7. (31 July 2009), e1000424. by William S. Noble posted to organization programming tutorial by apaydin on 2009-08-03 06:57:45 as along with 56 people and 7 groups pekrau Sergey_gerbek mordiano remoteFuture Yanno aaltenburger marekrud guhjy dolchan frohike operon CorinYeats artaban421 antonkratz tomhebbron maren bayesian daveGerrard JoeBanks jcaddy somak bertelsen ptrobajo nperoni daforerog mmwoodman charris5 GustavoLacerda pmendes fgibson rdiaz Zephyrus heliopais franklu310 lmichan silberbauer leemond31 jlangdon robfsouza Stew pmung reyez kshameer djkt pawelsobko jjray dswan renatomilani VGreiff cabbagesofdoom wei_tang fenghezi cisevol barry sdaehne druvus Pedro Martinez EvoDevo lab Barcelona Orengo Group Journal Picks Bioinformatics - CRUK ccsbs BergmanLab structural_bioinformatics McCammon
	Sampling Bottlenecks in De novo Protein Structure Prediction. [My Copy] Journal of molecular biology (28 July 2009) by David E. Kim, Ben Blum, Philip Bradley, David Baker posted to protein_structure_prediction sampling by apaydin on 2009-07-30 11:32:51 as along with 3 people and 2 groups barry siggi84 reyez structural_bioinformatics McCammon
	Efficient algorithms to explore conformation spaces of flexible protein loops. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 5, No. 4. (c 2008), pp. 534-545. by P. Yao, A. Dhanik, N. Marz, et al.R. Propper, C. Kou, G. Liu, H. van den Bedem, J. C. Latombe, I. Halperin-Landsberg, R. B. Altman posted to conformational_sampling loop by apaydin on 2009-07-30 10:28:07 as along with 1 person oteri
	Improving Structure-Based Function Prediction Using Molecular Dynamics [My Copy] Vol. 17, No. 7. (15 July 2009), pp. 919-929. by Dariya S. Glazer, Randall J. Radmer, Russ B. Altman posted to function_prediction molecular_dynamics structural_ensemble by apaydin on 2009-07-28 05:28:03 as along with 1 person and 2 groups barry structural_bioinformatics McCammon
	An introduction to scripting in Ruby for biologists. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009), 221. by Jan Aerts, Andy Law posted to programming ruby by apaydin on 2009-07-27 14:26:02 as along with 25 people and 3 groups isimpson kshameer n00c Zephyrus nuin sobolevnrm jago lwaldron natstreet Stew silberbauer mfenner phoenixzxl renatomilani abhishek_tiwari rschulz sjcockell dullhunk druvus neils daforerog fgibson leemond31 brianb dswan Bioinformatics - CRUK Journal picks Bioinformatics
	Using generalized ensemble simulations and Markov state models to identify conformational states [My Copy] Methods, Vol. 49, No. 2. (3 October 2009), pp. 197-201. by Gregory R. Bowman, Xuhui Huang, Vijay S. Pande posted to markov_chains srs by apaydin on 2009-07-19 17:16:11 as along with 1 person Diego_Prada
	NOESY-Based Strategy for Assignments of Backbone and Side Chain Resonances of Large Proteins without Deuteration [My Copy] Nature Protocols (2006) by Xu posted to assignments nmr by apaydin on 2009-07-13 10:51:21 as
	De novo protein structure determination using sparse NMR data [My Copy] Journal of Biomolecular NMR, Vol. 18, No. 4. (1 December 2000), pp. 311-318. by Peter M. Bowers, Charlie E. M. Strauss, David Baker posted to nmr protein_structure_determination by apaydin on 2009-07-10 08:20:56 as
	CheckShift improved: fast chemical shift reference correction with high accuracy [My Copy] Journal of Biomolecular NMR by Simon Ginzinger, Marko Skočibušić, Volker Heun posted to chemical_shift nmr by apaydin on 2009-07-09 12:54:26 as along with 1 person viktor21614
	Blind docking of pharmaceutically relevant compounds using RosettaLigand [My Copy] Protein Science, Vol. 18, No. 9. (24 June 2009), pp. 1998-2002. by Ian W. Davis, Kaushik Raha, Martha S. Head, David Baker posted to docking ligand-protein-binding by apaydin on 2009-07-04 08:48:01 as along with 1 person klexa
	Nature of the protein universe [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 27. (7 July 2009), pp. 11079-11084. by Michael Levitt posted to protein review by apaydin on 2009-07-04 08:45:08 as along with 9 people and 1 group martainn pmung ldiambra VGreiff carlosjavierna philcarter TRHvidsten paulschlesinger renatomilani Orengo Group Journal Picks
	TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. [My Copy] Journal of biomolecular NMR, Vol. 44, No. 4. (August 2009), pp. 213-223. by Yang Shen, Frank Delaglio, Gabriel Cornilescu, Ad Bax posted to backbone nmr prediction torsional_angle by apaydin on 2009-06-26 09:38:32 as along with 4 people dgront laurabailey viktor21614 anna_yershova

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nmr	188
protein	108
protein_dynamics	106
protein_folding	66
folding	51
review	51
protein_structure_determination	43
assignments	39
structure	39
protein_ligand_binding	34
protein_design	26
rdc	26
prediction	18
protein_protein_binding	18
resonance_assignment	18
tutorial	18
dynamics	16
normal_mode_analysis	15
allostery	14
chemical	14
rate_determination	14
unfolded_state	14
backbone	13
determination	13
phi_value_analysis	13
prm	13
model	12
pfold	12
nma	11
noe	11
misfolding	10
rate	10
shift	10
flexibility	9
ligand-protein-binding	9
molecular_dynamics	9
noe_assignment	9
protein_structure	9
sba	9
x-ray	9
design	8
docking	8
motion	8
voting	8
database	7
function	7
homology	7
molecular	7
probabilistic_roadmaps	7
rate_prediction	7
rotamer_libraries	7
sampling	7
algorithms	6
alignment	6
conformational	6
ensemble	6
go_model	6
planning	6
protein_protein_interactions	6
rotamer	6
srs	6
unassigned_nmr_data	6
based	5
binding	5
chemical_shift	5
enm	5
ensembles	5
markov_chains	5
monte_carlo	5
nvr	5
programming	5
relaxation	5
resonance	5
scoring	5
sidechain	5
side_chain_flexibility	5
structural	5
4d-noesy	4
analysis	4
coarse_grained	4
denatured	4
drug	4
entropy	4
hiv_integrase	4
hydrogen_exchange	4
inverse_kinematics	4
kinetics	4
learning	4
ligand_flexibility	4
network	4
shifts	4
webserver	4
aggregation	3
backbone_flexibility	3
collision	3
consensus	3
denatured_state	3
diffusion	3
elastic	3
energy	3
enzyme_redesign	3
fast	3
fold_determination	3
gnm	3
integer	3
intermediate	3
linear	3
loop	3
molecular_replacement	3
order	3
parameter	3
pathways	3
protein_structure_prediction	3
python	3
rigidity	3
saxs	3
search	3
simulations	3
teaching	3
torsional_angle	3
transition_state_ensemble	3
acbp	2
annealing	2
ant	2
approximation	2
bipartite_matching	2
cap	2
cheminformatics	2
closure	2
colony	2
comparison	2
contacts	2
corex	2
couplings	2
data	2
detection	2
diversity	2
efficient_energy_minimization	2
energy_landscape	2
equilibrium	2
finkelstein	2
fold	2
fragment	2
funnel	2
genetic	2
gpcr	2
hotspot	2
hp	2
hydrogen_bonds	2
incremental	2
index	2
inverse	2
kinematics	2
kstar	2
landscape	2
lattice	2
ligand	2
markov_random_field	2
mass_spectrometry	2
metadynamics	2
methods	2
mfpt	2
milestoning	2
modeling	2
modelling	2
molecular_mechanics	2
native	2
negative_design	2
noise_stability	2
nrps	2
optimization	2
path	2
phi	2
recognition	2
reference	2
replacement	2
secondary	2
simulated	2
solvation	2
solvent_effects	2
space	2
systems_biology	2
tool	2
transition	2
unfolded	2
value	2
visualization	2
xray	2
advice	1
anisotropic	1
anm	1
assembly	1
atomic	1
averaging	1
bayesian_methods	1
belief	1
benchmark	1
bpti	1
branch_and_bound	1
calculation	1
c-alpha	1
cdc25	1
charges	1
chevron	1
classification	1
cloud_computing	1
comment	1
communication	1
comparing_different_motion_models	1
complete	1
completeness	1
complex	1
component	1
configurational	1
conformational_sampling	1
constant	1
constraint_satisfaction	1
content	1
croem	1
cryo	1
crystallography	1
cyana	1
d-amino-acid	1
ddg	1
denovo	1
density	1
difference_map	1
dimensionality_reduction	1
dipolar	1
disordered	1
disordered_proteins	1
distance_measure	1
drug_design	1
drug_discovery	1
electron_microscopy	1
electrostatics	1
elnemo	1
em	1
empirical	1
empirical_scoring_function	1
energy_function	1
entropy_estimation	1
equation	1
essential_dynamics	1
evolution	1
example	1
exchange	1
experimental	1
experiments	1
fft	1
finding	1
flexibiliy	1
foldamer	1
folder	1
foldtraj	1
free	1
froda	1
functional_classification	1
function_prediction	1
geometric	1
geometry	1
germany	1
go	1
graph_cuts	1
graph_representation	1
graph_theory	1
hardware	1
hausdorff	1
hd_exchange_rate	1
homologous	1
information	1
initiative	1
inverse_folding	1
kariyer	1
kinetic	1
kl_distance	1
lambda	1
library	1
ligand_binding	1
linguistics	1
local	1
long	1
macromolecular	1
manipulation_planning	1
maps	1
mars	1
master	1
md	1
membrane	1
meta	1
metaheuristics	1
mining	1
mle	1
modeller	1
molecular_design	1
motif	1
mr	1
multidomain	1
multipole	1
multiscale	1
non-holonomic	1
opensource	1
opinion	1
optimum	1
organization	1
paramagnetic_quenching	1
partial	1
pattern	1
pca	1
peptides	1
perspectives	1
placement	1
plot	1
pnas	1
pre	1
principal	1
propagation	1
protein_dna_binding	1
protein_stability	1
psi-value-analysis	1
redcat	1
refinement	1
refolding	1
replica	1
repressor	1
research	1
residue	1
ribosome	1
rna	1
robotics	1
rosetta	1
ruby	1
scattering	1
score	1
scoring_function	1
screening	1
sequence	1
sequential	1
sh3	1
simplified	1
software	1
state	1
stochasticity	1
structural_ensemble	1
study	1
supercomputer	1
supramolecular	1
svm	1
synthesis	1
tabu	1
task_planning	1
tensor	1
thermodynamic	1
thermodynamics	1
time	1
tools	1
topology	1
ubiquitin	1
umbrella_sampling	1
waiting_time	1
water_hsqc	1
wavelets	1
wide-angle	1

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